rs2633306

Variant names:

• chr10-73892689-A-C
• rs2633306
• ENST00000746853.1:n.277-1074A>C

Your query was ambiguous. Multiple possible variants found:

• chr10-73892689-A-C
• chr10-73892689-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000746853.1(ENSG00000297292):​n.277-1074A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.701 in 152,084 control chromosomes in the GnomAD database, including 37,992 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.70 (37992 hom., cov: 32)
• Consequence: ENSG00000297292 ENST00000746853.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320
• Publications: 8 publications found

Genes affected

ENSG00000297292 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297292	ENST00000746853.1	n.277-1074A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.701 AC: 106506 AN: 151964 Hom.: 37968 Cov.: 32

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.687

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.753

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.701 AC: 106568 AN: 152084 Hom.: 37992 Cov.: 32 AF XY: 0.691 AC XY: 51375 AN XY: 74322

African (AFR) AF: 0.717 AC: 29736 AN: 41486

American (AMR) AF: 0.583 AC: 8905 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.882 AC: 3059 AN: 3468

East Asian (EAS) AF: 0.425 AC: 2193 AN: 5164

South Asian (SAS) AF: 0.592 AC: 2856 AN: 4824

European-Finnish (FIN) AF: 0.625 AC: 6601 AN: 10566

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.747 AC: 50772 AN: 67992

Other (OTH) AF: 0.746 AC: 1572 AN: 2108

Alfa AF: 0.688 Hom.: 13168

Bravo AF: 0.700

Asia WGS AF: 0.488 AC: 1699 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.2
DANN	Benign	0.38
PhyloP100		-0.032

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2633306; hg19: chr10-75652447;